In tomorrow’s New York Times, I take a look at the evolution of intelligence. Or rather, I look at its flip side. Scientists and the rest of us are obsessed with intelligence–not just the intelligence of our own species, but any glimmer of intelligence in other animals. I’ve written plenty of stories myself on this research, from the social brilliance of hyenas to the foresight of birds. But if these faculties are so great, then why aren’t more animals smart? The answer, experiments suggest, is that learning and memory have nasty side-effects. They can even shorten your life (at least if you’re a fly).

This story has an odd back-story of its own. If you report on scientific research on evolution, sooner or later you’ll find yourself reading mind-blowing distortions of the science produced by creationists and people who make the same sorts of distortions and really really really don’t want to be called creationists. Sometimes they happen to choose some interesting research to distort, which, for me, is the silver lining in gloomy creationist clouds.

A couple years ago I discovered to my surprise that Ann Coulter devoted several pages in one of her books to misreading an article of mine about the appendix. Coulter couldn’t seem to understand that despite natural selection’s ability to produce adaptations, nature is filled with flaws (like my own defective appendix). One source of nature’s imperfection is the inescapable trade-off between the benefits some traits provide and the costs they incur. Coulter scoffed at experiments that suggested natural selection might not favor smart fruit flies. At about that point, I decided I had enough of Coulter and tracked down the original studies. I’ve been following this fascinating line of research ever since.

In my last post I wrote about how scientists are learning about the origin of animals by studying their genomes. One of the surprising findings of the latest research is that a group of animals called comb jellies (ctenophores) belong to the oldest lineage of living animals. Comb jellies look a bit like jellyfish–soft, tentacled creatures without brains or eyes but with a nervous system. As I wrote in the Boston Globe Monday, earlier studies had generally pointed to sponges as belonging to the oldest lineage. If comb jellies take their place, that may mean that the ancestors of sponges lost their nerve(s) and became anchored filter-feeders.

IMHO the tree is full of long-branch attraction. The position of the ctenophores is probably spurious.

So what’s David talking about? Long-branch attraction refers to a pesky problem that evolutionary biologists face when trying to reconstruct ancient episodes in the history of life. In my article I only referred briefly to these sorts of challenges, but fortunately blogs give me a little room to stretch out.

Long-branch attraction is a new twist on a classic phenenomon in evolution called convergence. This happens when two lineages evolve into very similar forms. Legless lizards and snakes, for example, independently evolved a serpent body shape. The octopus eye forms images like a camera, just as ours do. Several strains of E. coli have evolved into disease-causing bacteria that invade intestinal cells. On the surface, two convergent species may look as if they share a close common ancestry. It can take some close scrutiny to discover that they are not.

A segment of DNA can also evolve convergenty in two lineages. Imagine that a particular segment of DNA in the ancestors of insects had a sequence, AAATAAA. Imagine that vertebrates had a sequence AATTGAA. It takes only one mutation in each lineage for them to both evolve into AAATGAA. Now they have an identical segment that they did not inherit through common ancestry.

This sort of convergence is unlikely to happen soon after two lineages split apart. But as more time passes–as branches get longer–it becomes more likely. Branches that are not in fact closely related get attracted to each other when scientists study their DNA. Hence, long-branch attraction. In the case of this new study, David is suggesting that sponges ended up looking more closely related to us than comb jellies because the DNA the scientists studied happened to evolve convergently.

I dropped a note to Casey Dunn, the lead author of the new study in Nature, and he fired back some enlightening comments…

Long branch attraction is one of the most common types of systematic error encountered in phylogenetic inference…It is the primary reason we say in the paper that the ctenophore result “should be viewed as provisional”. Unfortunately, the Nature format is very restrictive in its length so we did not have room to explicitly discuss this issue, though we were very mindful of it and much of the experimental design was structured specifically to address it.

That design included finding lots of weird animals. Adding branches to an evolutionary tree essentially chops down long branches to shorter lengths, because the new species are more closely related to some of the animals than to others. That’s why one of Dunn’s colleagues fished up a second species of comb jelly when the startling results first emerged. The long branch of the original comb jelly now became split in two, reducing the amount of long-branch attraction.

Another possibility might be that the ancestors of comb jellies have evolved faster than other animals. Their rapid evolution would give rise to more differences between their DNA and the DNA of other animals. As a result, the more slowly-evolving animals, including sponges and us, would appear more similar. But when they measured the rate of change on each branch, the comb jellies didn’t appear at all peculiar.

By taking these extra steps (and others), Dunn and his colleagues felt confident enough to go into print with their results. Fortunately, scientists can continue to test for the possibility of long-branch attraction by adding more species to the tree. Animals that belong to deep lineages are the best. The bizarre, balloon-bodied Trichoplax would be a good place to start, since its genome is already sequenced. Science, thankfully, marches on.

Today in the Boston Globe, I write about how scientists are revising their understanding of the evolution of animals, thanks to more DNA and more weird animals. My favorite quote comes from biologist Mark Pallen, who says that the human genome would have been worthless without understanding how humans are related to other animals.

Unfortunately, this research has been subject to some poor reporting, and to some distortions from creationists. Ryan Gregory and Troy Britain set them straight, respectively.

NOTE: I’VE SET UP A FLASH VERSION OF THIS TALK HERE. DON’T BOTHER TRYING TO DOWNLOAD THE QUICKTIME VERSION I DESCRIBED IN THIS POST.

Recently I gave the Discovery Lecture at Carleton University in Ottawa, in which I talked about new developments in evolutionary biology. They sent me a DVD of the talk, and I got a lunatic notion in my head that I would figure out how to get all Web Two-Point-O-Ee and post the lecture online. They told me to go ahead as long as I put a watermark on. Ever eager to waste time, I slowly figured out how to do that on QuickTime. Then I uploaded it to blip.tv, because they let you post big files. But that’s where my superduper tech acumen falls apart, because for some mysterious reason the site won’t convert it into a sleek, embeddable Flash format. If you don’t mind the somewhat less sleek QuickTime, here’s the talk.

(If anybody wants to teach this tech cub a lesson or two on how to do this sort of thing, I’m all ears.)

I’m particularly fond of their latest podcast, which you can listen to below. It’s about chimeras, synthetic biology, and other threats to our conventional notions of life.

Full disclosure: I am acquainted with Robert Krulwich, one of the hosts, and in recent months he and I have spent a fair amount of time talking about the brave new world of synthetic biology. He is freaked out in many ways, some legitimate, and some, I think, not so much. (I recently wrote about why I can’t summon up a good freak-out in Wired.) Bascially, I think ordinary biology like foul drinking water and drug-resistant bacteria is more frightening than a microbe that smells like wintergreen. But you can listen to Krulwich get disturbed and judge for yourself.

I’ve been writing about biology for quite some time now, and sometimes I think I’ve got a pretty good sense of the scope of life. Neurosurgeon wasps–got it. Eels with alien jaws–check. And then I stumble across something new, or should I say, new to me.

This week’s revelation is androgenesis. Androgenesis is what happens when kids get all their genes from their father. Normally humans and other animals produce offspring by combining DNA from both mother and father, an arrangement that’s often the case in plants as well. Both sperm and eggs only get one of the two copies of each chromosome in the genome. When male and female gametes combine, they have enough DNA together to make a new organism. There are exceptions. Hermaphrodites can be fathers or mothers. Then there’s parthenogensis, in which a female animal’s eggs begin developing into embryos without any sperm carrying Dad’s genetic delivery. I thought that this represented the outer edge of strange kinds of reproduction. And then I came across androgenesis.

At first I couldn’t even imagine how androgensis can work. How can you start growing an embryo from a sperm, I wondered? And while I could at least imagine that a man might bear a child if an embryo was implanted in his gut, I could not understand how this could happen in any animal naturally. But of course, I should know never to rely on my feeble powers of imagination to guess at the maximal weirdness nature can deploy. (I probably shouldn’t have posted this on April 1, because people may think I’m joking. I’m not.)

Androgenesis, it turns out, transforms fatherhood into a parasitic invasion. It begins like normal fertilization, with a sperm fusing to an egg. But then the egg’s DNA gets hurled out of its nucleus, so that the sperm’s genes are the only ones left in the egg. The egg begins to develop into an embryo, but only after it has lost the mother’s DNA.

Androgenesis is rare in the natural world, but it’s not obscure. Asian clams (Corbicula) came to the United States several decades ago, possibly by Chinese immigrants for food. Today they’re a major pest. And two of the species that have come to our shores use androgenesis to reproduce. These particular Asian clams are hermaphrodites. Along with eggs, they also make sperm–but these are odd sperm, with a full supply of DNA. Once their sperm has fertilized the egg of another clam, the female DNA is ejected, and the clam embryo starts to develop. The mother clam broods father’s clones in her gills, where they can probably thrive on the food that gets trapped there.

To be precise, the eggs of Asian clams don’t lose all their DNA. Most of the DNA in animal cells is in the nucleus, but there are also dozens of little energy-generating factories in the cell called mitochondria that carry their own bits of DNA as well. Fathers evict the maternal DNA from the nucleus, but the mitochrondial DNA stays behind. This only makes sense (insofar as androgenesis makes much sense at all), because a cell without a way to generate energy would have a hard time growing into an embryo.

Scientists can build evolutionary trees from DNA, using it to determine how individual animals are related to one another. But when they build the tree of invasive Asian clams, the mitochondrial and nuclear DNA reveal different genealogies. It looks as if the two invasive species have been carrying out androgenesis on each other.

The ability Asian clams have to use other species to make near-clones of themselves may help resolve one of the paradoxes of androgenesis. Once androgenesis arises in a species, it should be able to spread quickly because the fathers can reproduce so much faster than more conventional clams. Taking the female side of this deal is a losing proposition, because females can’t pass their DNA down to the next generation. So androgenesis ought to lead to swift extinction, like some sort of paternal plague. Even if androgenetic animals could somehow avoid this doom, they would bear another burden: mutations. Without the benefit of sex to mix up their DNA, they would accumulate harmful mutations over the generations that could threaten the survival of the entire population.

The huge success of Asian clams in the US is proof that androgenesis is not a one-way ticket to oblivion. Androgenesis may survive in part because the fathers can make other species their victims, too. Another species can offer an extra supply of eggs, as well as an extra supply of DNA. Studies on the DNA of Asian clams in the US suggest that on rare occasion, some of the mother’s DNA stays behind in the egg. This fresh influx of genes may rescue androgenetic clams from some of their harmful mutations.

For more information on androgenesis, check out this new paper in the journal Evolution. And if any biologists are holding out on any other bizarre biology, it’s time to come forward.

Hyenas are fascinating in many ways, such as the way female spotted hyenas are equipped with a penis of sorts (pdf). In tomorrow’s New York Times, I look at a new kind of fascination: hyena brains. Hyenas have a remarkably complex social life, and it appears to have altered the shape and size of their brains. The same social forces were at work in our own ancestors. Humans and hyenas, in other words, have been rolling on parallel evolutionary tracks.

For further details, check out the densely packed web site of Kay Holekamp, the biologist who has been investigating the social hyena brain. And don’t miss the slide show the Times has put together for my article.